stem to procedure_occurrence

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flowchart LR
    subgraph Source
        finngenid
        source
        approx_event_day
        code1
        index
        omop_source_concept_id
    end

    subgraph CDM-OMOP-v5.4
        person_id
        procedure_date
        procedure_end_date
        procedure_source_value
        procedure_source_concept_id
        visit_occurrence_id
    end

    finngenid-->person_id
    approx_event_day-->procedure_date
    approx_event_day-->procedure_end_date
    source-->visit_occurrence_id
    index-->visit_occurrence_id
    code1-->procedure_source_value
    omop_source_concept_id-->procedure_source_concept_id

Destination Field	Source field	Logic	Comment field
procedure_occurrence_id		Incremental integer. Unique value per each row procedure_occurence.	Generated
person_id	finngenid	person_id from person table where person_source_value equals finngenid	Calculated
procedure_concept_id		concept_id_2 from concept_relationship table where concept_id_1 equals procedure_source_concept_id and relationship_id equals “Maps to”	Calculated NOTE: IF a procedure_source_concept_id has more than one standard mapping (concept_id_2), one row is added per each additional procedure_concept_id
procedure_date	approx_event_day	Copied from approx_event_day	Copied
procedure_datetime		Calculated from procedure_date with time 00:00:0000	Calculated
procedure_end_date	approx_event_day	Copied from approx_event_day	Copied NOTE: There is no procedure_end_date in the source data, it is set same as procedure_date
procedure_end_datetime		Calculated from procedure_end_date with time 00:00:0000	Calculated
procedure_type_concept_id		Set 32879 - ‘Registry’ for all	Calculated
modifier_concept_id		Set 0 for all	Info not available. NOTE: Info potentially available: Perhaps the some nomesco codes should be mapped to modifier vocabulary and used in here. To discuse with FinOMOP.
quantity		Set 1 for all	Calculated
provider_id		provider_id for mapped visit_occurrence_id from visit_occurrence table.	Calculated
visit_occurrence_id	source index	Link to correspondent visit_occurrence_id from visit_occurrence table where visit_source_value equals “SOURCE=source;INDEX=index”.	Calculated
visit_detail_id		set NULL for all	Info not available
procedure_source_value	code1	Copied code1 as it is	Copied
procedure_source_concept_id	omop_source_concept_id	IF omop_source_concept_id is not null then omop_source_concept_id ELSE 0	Calculated
modifier_source_value		Set NULL for all	Info not available